Module: Bio::Map

Defined in:

lib/bio/map.rb

Overview

Description

The Bio::Map contains classes that describe mapping information and can be
used to contain linkage maps, radiation-hybrid maps, etc. As the same
marker can be mapped to more than one map, and a single map typically
contains more than one marker, the link between the markers and maps is
handled by Bio::Map::Mapping objects. Therefore, to link a map to a marker,
a Bio::Map::Mapping object is added to that Bio::Map. See usage below.

Not only maps in the strict sense have map-like features (and similarly not
only markers in the strict sense have marker-like features). For example, a
microsatellite is something that can be mapped on a linkage map (and hence
becomes a 'marker'), but a clone can also be mapped to a
cytogenetic map. In that case, the clone acts as a marker and has
marker-like properties. That same clone can also be considered a
'map' when BAC-end sequences are mapped to it. To reflect this
flexibility, the modules Bio::Map::ActsLikeMap and Bio::Map::ActsLikeMarker
define methods that are typical for maps and markers.

– In a certain sense, a biological sequence also has map- and marker-like
properties: things can be mapped to it at certain locations, and the
sequence itself can be mapped to something else (e.g. the BAC-end sequence
example above, or a BLAST-result). ++